Mitochondrial marker-based insights into the genetic diversity and population connectivity of the vulnerable (IUCN Red List) snow trout (Schizothorax plagiostomus) from the Tons River, Western Himalaya

Introduction Advanced molecular tools have a significant role in the growth of sustainable aquaculture systems. Their immense contribution is particularly notable among cold-water fish in the Himalayan regions, where available genetic data is limited. Methodology This study aimed to evaluate the specific characteristics, such as genetic diversity and population structure, of vulnerable Schizothorax plagiostomus (Cyprinidae) in the Tons River, a major tributary of the Yamuna River in Uttarakhand. Mitochondrial markers, namely COI and Cytb , were utilised for the analysis. Results In this study, a total of 40 S. plagiostomus sequences, from concatenated COI and Cytb (762 bp), were analysed. Major findings observed 10 haplotypes in COI and 12 in Cytb , indicating relatively higher diversity in Cytb than in COI. Whereas 20 haplotypes were observed in the concatenated sequences, representing overall moderate genetic diversity among populations. Conclusion S. plagiostomus is listed as a vulnerable species on the IUCN Red List. This study revealed that despite historical population declines, the species still retains considerable genetic variation. Conserving this existing moderately high genetic variation is important for maintaining the long-term evolutionary potential of this species. This study provides the first mitochondrial baseline data for S. plagiostomus in the Tons River. And also demonstrates how genetic markers function as advanced tools for conservation and sustainable aquaculture development in Himalayan cold-water species. The moderately high mitochondrial diversity observed suggests the presence of diverse maternal lineages. However, further investigation using nuclear markers is required to fully assess genetic diversity and cryptic structure. Furthermore, the study demonstrates the usefulness of mitochondrial markers for assessing genetic diversity.